RefRGim: an Intelligent Reference Panel Reconstruction Method for Genotype Imputation with Convolutional Neural Networks

Shuo Shi,Qiheng Qian,Shuhuan Yu,Qi Wang,Jinyue Wang,Jingyao Zeng,Zhenglin Du,Jingfa Xiao

Briefings in Bioinformatics（2021）CCF BSCI 2区

Chinese Acad Sci | Qujiang Culture Finance Holding Grp Co Ltd

Cited 4|Views29

Abstract

Genotype imputation is a statistical method for estimating missing genotypes from a denser haplotype reference panel. Existing methods usually performed well on common variants, but they may not be ideal for low-frequency and rare variants. Previous studies showed that the population similarity between study and reference panels is one of the key factors influencing the imputation accuracy. Here, we developed an imputation reference panel reconstruction method (RefRGim) using convolutional neural networks (CNNs), which can generate a study-specified reference panel for each input data based on the genetic similarity of individuals from current study and references. The CNNs were pretrained with single nucleotide polymorphism data from the 1000 Genomes Project. Our evaluations showed that genotype imputation with RefRGim can achieve higher accuracies than original reference panel, especially for low-frequency and rare variants. RefRGim will serve as an efficient reference panel reconstruction method for genotype imputation. RefRGim is freely available via GitHub: https://github.com/shishuo16/RefRGim.

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Key words

genotype imputation,reference reconstruction,deep learning,genome-wide association study

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